Confusion: The Beginning
by Lady Katana4544
Summary: The TMNT are ambushed by a new enemy and one of the turtles is taken hostage. Will their brother fall to the Dark Power? And will his family be able to find and rescue him? First story in the Confusion series. Chapter 2 is now up!
1. Fight and Capture

**Disclaimer: I don't own any of the TMNT or their allies. If I did that would be way awesome, but I don't. So yeah everything in this story including the story line belongs to me.**

**Note: This revised version of the story still has all the same characters. I have revised the story a little and I am going to try and make the chapters longer than they were in the original version.**

**Anyways onto chapter one! **

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**Chapter 1: Fight and Capture**

A woman wearing armor, a dark cloak and a mask over her face, stood on top of a tall building, her second-in-command stood calmly behind her. Behind them both were their shadow soldiers kneeling on the hard roof top, waiting to be given their orders for the mission.

The woman soon opened her eyes and looked through her mask at the stars that were positioned above them. Then something in her mind whispered to her, telling her that her prey, her choice of capture was now coming towards their position and location. She then turned the man behind her, his dark eyes staring through his own mask at the ground in front of him; she cleared her throat to get his attention drawn to her. She nodded to him slightly and silently, which in turn he then turned back to their warriors and gave them all a simple command to follow.

"It is now time. Move into your positions."

The shadow soldiers got up off of their knees and quickly bowed, before they silently moved into different positions on different buildings, but sticking close to the one that they would soon spring their trap on their soon to be victims.

Leonardo was leading his brothers on a patrol run through the city, he had been wondering if it had been a good idea at all to leave to the Lair at all. But his younger brothers had been itching to go back to surface for a good three months now, which had been getting on their Master's nerves and wearing down his patience with them all, but they were also in some way, needed by the people of New York City for protection from the gangs that were constantly perusing the city, always looking to cause some sort of trouble. Then something suddenly prickled at the edge of his senses and he then suddenly stopped in place, making his brothers quickly stop behind him, so that they didn't knock each other or him down onto the roof. His brothers watched him in complete and utter silence as Leo searched the area around him with his eyes and inner senses as he unsheathed his twin katana blades at the same time.

Leo's eyes suddenly widened as he saw what coming towards him and his brothers, he then pushed his brothers away from him, before he leaped away as well, which wasn't a second too soon before several shuriken took places at where he had been standing just a second before.

Raphael looked up and found to his immense surprise that he nor his other brothers were anywhere near each other and that there were numerous warriors in black separating them from each other. He absently noticed as he fought that most of the dark warriors were going after Leo, he had then had to shake himself mentally, so that he didn't get skewered by an enemy sword. As Raphael fought his batch of dark soldiers, he found that he was close enough to his other two brothers and observed them out of the corner of his eye as he fought. Both Mikey and Donnie were holding their own against the warriors that they were fighting, but he wasn't really sure about how much longer that they would both be able to fight.

The masked woman turned to her companion, her eyes glowing angrily, the fight in the beginning when her warriors had ambushed the four turtle creatures, the fight had been going their way, but now the fighting seemed to be leaning more in the turtle's favor every second that they stayed there on the rooftop fighting. The woman knew that if they didn't take what they wanted and fast that she wouldn't be able to get another chance at anything ever again. Her voice then sounded out from behind the mask and reached her companion's ears through the fighting.

"Distract the turtle in blue long enough for me to get close enough to him and drug him."

The man quickly bowed and moved even more quickly towards Leonardo's position. Leo was very surprised when the masked man had suddenly appeared in front of him and began fighting with him. But unbeknownst to him, the woman who had ordered the man to attack Leo was now grinning behind her mask and was quickly able to get close to enough to subdue him with the drugs. Leo to both his horror and surprise felt something sharp prick the back of his neck. He dropped his katanas and he fought to stay upright, but he soon collapsed down onto the roof, but before he completely succumbed to the drugs, he managed to weakly call out one of his brother's names before he passed out completely.

"Raph…help…Raph."

Raphael heard his elder brother call to him and looked over in his direction just in time to see his brother be taken by the masked villains, who were soon followed by their soldiers who were uninjured in the fight, leaving only Leo's twin katanas behind. Most of their attacker had been either hurt, injured or lay dying in a pool of their own blood that mingled with the blood of their fellow warriors in arms. Don and Mikey soon joined their older brother as Raph bent to gently and carefully pick up their brother's fallen weapons. As they were leaving the building to enter the sewers and their home to tell their Sensei the news of Leo's capture; a low moan broke the silence around them, which came from one of the injured warriors.

Donatello quickly moved to the one warrior that he had heard groan and found that the warrior was out cold, which even the warrior was out cold, the soldier had a strong grip on another soldier's wrist that lay close by. He quickly bound the two warriors together with rope and helped Mikey get them down the side of the building.

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-Kraishi Ninja Base-

The masked man appeared about a minute or two later, with Leo, who was still out thanks to the drugs that were now in his system, that had been used by the Lady. He with the help from one of the underlings tied the turtle between two poles, making sure that the turtle was held between them securely, like he was almost standing between them, but his toes barely touched the floor. Then the masked woman appeared behind them, the man and the underling bowed swiftly, before the underling vanished in a puff of smoke, while the woman took her place beside the man and stared at their prize, the man then stood up and stood beside.

"Has the turtle awoken since we took him from the fight?"

"No he has not, m'lady."

Then a battered and bruised Leo suddenly stirred, weakly groaned and opened his eyes. Once he had fully awoken, he noticed that he wasn't alone and saw them, before he attempted to glare at them. To his surprise, the female figure suddenly lashed out at him, cutting the left side of his face and punched the turtle's stomach, making Leo groan in pain from the first attack. He sagged a little or tried to, but the rope and the poles defeated that purpose as he tried to regain control of his breathing, before he then attempted to lash at them. Leo managed to kick up his legs and tried to knock the woman onto the floor, but the woman jumped back up and had backhanded the right side of his face, she then grabbed his mask tails and smacked his head really hard with another pole.

"Try to do something like that again to me and your pain will only be increased more, you freak.", hissed the woman

She then added. "Drug him again."

The woman grinned gleefully from behind her mask as she watched an underling appear and give a syringe to the man, before disappearing again, and as the turtle went under again from the drugs and the pain of his injuries. She then turned and walked out of the room, not really caring that her second-in-command was close behind her, once the doors to the chamber were closed, she then magically sealed the doors shut, before she turned her attention to the man.

"Put two of our best soldiers to guard the door. No one but you or myself may enter this room."

The man bowed.

"As you wish it to be done, m'lady. Your command shall be done and full filled."

She then turned and disappeared down the hall. The man turned and then chose to two of their best soldiers to guard the door and their prisoner.

The woman then entered her chambers about two minutes later. She then decided to meditate and watch the turtle's spirit in the astral plane.

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**To Be Continued**

**What did you think? **

**Chapter Two is already written and I will begin typing it up soon.**


	2. Discovery and A Plan

Disclaimer: I don't own any of the TMNT or their allies

**Disclaimer: I don't own any of the TMNT or their allies. If I did that would be way awesome, but I don't. So yeah everything in this story including the story line belongs to me.**

**Note: This revised version of the story still has all the same characters. I have revised the story a little and I am going to try and make the chapters longer than they were in the original version.**

A/N: Well looks like I'm finally starting to get this story back up and running. I'm pretty much finally getting around to putting chapter 2 up and the next chapters will up soon.

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**Chapter 2: Discovery and A Plan**

**The Lair**

Master Splinter was sitting and drinking some of his herbal teas while he listened for sounds of his sons as they returned to their sewer home. When he found that his sons were silent, it was something that he found disturbing and disconcerting as his youngest son was always the loudest of his brothers.

Then he heard the door of their home be slammed open and he stood up to see his second oldest son Raphael walk in carrying Leonardo's twin katanas and he was followed in by Donatello and Michelangelo came in, both of the brothers were carrying a person each between them.

"My sons, what has happened to Leonardo? Who are these two people?"

Raphael knelt before Splinter, while Donnie and Mikey put the two people nearby before they joined Raphael and their master, Donnie knelt on Raphael's right and Mikey knelt on Raphael's left. Raph looked at Don and Mikey as though he was seeking their permission before Don slowly nodded and Raph sighed softly.

"Sensei, we were ambushed while we were out on patrol. This new enemy was able to successfully separate up from each other. They were able to somehow to subdue Leo and they took before we could even stop them."

Splinter was shocked and filled with anger, how dare someone attack his family and take one of his precious sons from him. They would pay dearly for committing this act upon his family. Splinter mentally shook himself and took a long calming breathe, before he looked over his sons at the injured warriors.

"And what of these two warriors, my sons? Are they our prisoners as Leonardo is their leader's prisoner?"

Raph looked at their sensei in surprise before he finally noticed that they had taken prisoners. He looked at Don, who meet his gaze before the purple clad turtle broke the shared look and looked to their sensei and bowed his head close to the floor as he sought permission from their sensei to speak.

"You may speak, Donatello."

Donnie moved back into a upright kneeling position, gathering his thoughts together in an accurate order.

"Sensei, since Leo was taken as a hostage by the enemy, it may be prudent to have a hostage or two of our own. Also these two are injured, so if we were to take care of them and help them recover at least half of their normal strength. Then we might be able to help them help us get Leo back."

Splinter nodded but felt that a trip to the astral plane would be helpful in helping them put their plans together.

"Very well then my sons. Let us journey to the astral plane together, so we can put this plan into action and rescue their brother."

Splinter got up and slowly, but somewhat hurried to the center of the dojo with his three sons following at a somewhat slower pace. They knelt in a semi circle around their master and eased themselves into meditation.

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**Astral Plane**

The masked woman, known as Lady Micra, the leader of the New Dark Dragons watched the astral form of the turtle known as Leonardo but she kept herself hidden from his ninja senses. But another person also watched him as well and yet she knew that Micra was there. This other person was a little girl named Yutsuko. Yutsuko had been found by Micra's second and he had done something that had forced her from the beginning to share her body with Micra. After they had been put together through the magic, Yutsuko had learned and discovered that Micra was an ancient witch, who had lived in Feudal Japan.

They both disliked each other passionately for many many reasons. Micra sensed that more astral presences were coming and thoroughly blocked them as Yutsuko took form and quickly moved to Leo's side as he was started to stir. Micra paid them very little attention as she sent Splinter and his other sons back into their bodies. She didn't need them interrupting her work with the injured turtle as she then turned her attention back to them and finally noticed that Yutsuko and the turtle were talking.

"Where am I?", Leonardo asked dazedly

"The astral plane, I think. My name is Yutsuko. Who are you?", answered Yutsuko curiously

"I am called Leonardo or Leo by my brothers. Why is a little girl like you here though?", answered Leo

At his simple question, Yutsuko felt or rather sensed that Micra froze. She then mentally smirked and then tried to answer his question. She knew that Leo could only sense her presence and not Micra's presence.

"You remember the masked person who had attacked you earlier on the physical plane?"

At Leo's cautious yet firm nod, she felt encouraged to continue onwards and decided to speak again.

"Well her name is Lady Micra, she and I share my body… Oh no! She is here!"

Micra now very angry showed herself with her mask on her face as an unseen wind blew around them. She glowered through her mask at the cowering form of Yutsuko.

"You disgust me, you pathetic child! I shall punish you later."

Yutsuko's eyes widened in terror as she cowered before the evil witch.

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**The Lair**

Back in the sewer lair, Master Splinter was surprised that they had been blocked from the astral plane while his sons were almost numb with shock.

"Masta what just happened?", asked Raph

"I do not know, my son. It seems that someone does not want us there.", answered Splinter

Then another voice spoke up and surprised them.

"Then that means, O great leader is hard at again."

**TBC.**

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_A/N: Wow looks like I have finally updated again. I don't know how long it will take me to get chapter 3 and up typed up and posted._


	3. author notice

Just a small little note: ^^

You may have noticed that I have fallen behind on updating some of the chapter fics that I have on here. I do apologize for that and I'm not really sure what the reasoning is behind that other than I can't upload a new chapter say for fics _Defend and Protect_ (TF) or any of my TMNT chapter fics or even my Star Wars, _The Lie_.

But really the point of this note is that my fics are being updated at my comm, tender_writings, on LJ. http: // community. livejournal. com / tender_writings

I will however keep trying to update things here if by some reason, you can't read the stuff on the comm, so I won't be deleting this account anytime soon as i'm using it now to keep track of some interesting authors in different fandoms of interest.


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